Well to be honest, as GM you create the background and, with that, the resources, intel, and knowledge that each NPC or group has in that background. When you get right down to it, as a GM you choose who is easiest to grab. Sure, the mage might be able to rain holy hell down if he notices the guys coming to nab him, but there are all manners of nabbing someone. A Tranq patch on a crowded subway platform, a slab dart from across the street as he unlocks his door, the classic snatch and grab with a magemask/collar, or even a simple one two sucker punch on the street.
I'm not saying that mages are always the easiest target, but easiest target is likewise not just easiest to physically get, but also who is easiest/most convenient/most efficient to get. There are likewise plenty of ways of containing a mage and even keeping them from being a threat while contained. And for the not so nice, popping the mage's eyes and blindfolding them can cause some nasty havoc too.
As for asking permission, do I have to ask permission for guard's to use Smartlinks too? I mean that just sounds ridiculous. I can understand asking at the beginning of the campaign "Do you guys want to play, I'm a rough GM." Anything more than that is just flat out unneeded.